Related papers: Predicting Non-Equilibrium Folding Behavior of Pol…
We study rough high-dimensional landscapes in which an increasingly stronger preference for a given configuration emerges. Such energy landscapes arise in glass physics and inference. In particular we focus on random Gaussian functions, and…
Complex dissipative systems appear across science and engineering, from polymers and active matter to learning algorithms. These systems operate far from equilibrium, where energy dissipation and time irreversibility govern their behavior…
We use Wang-Landau and replica exchange techniques to study the effect of an increasing stiffness on the formation of secondary structures in protein-like systems. Two possible models are considered. In both models, a polymer chain is…
We study the equilibrium properties of a flexible homopolymer where consecutive monomers are represented by impenetrable hard spheres that are tangent to each other, and non-consecutive monomers interact via a square-well potential. To this…
A variety of methods are developed for characterising the free energy landscapes of continuum, Landau-type free energy models. Using morphologies of lipid vesicles and a multistable liquid crystal device as examples, I show that the methods…
Within the framework of imaginary-time evolution for matrix product states, we introduce a cluster version of the infinite time-evolving block decimation algorithm for simulating quantum many-body systems, addressing the computational…
The thermodynamic entropy of coarse-grained (CG) models stands as one of the most important properties for quantifying the missing information during the CG process and for establishing transferable (or extendible) CG interactions. However,…
Energy landscapes are high-dimensional surfaces representing the dependence of system energy on variable configurations, which determine crucially the system's emergent behavior but are difficult to be analyzed due to their high-dimensional…
Metropolis algorithm has been extensively employed for simulating a canonical ensemble and estimating macroscopic properties of a closed system at any desired temperature. A mechanical property, like energy can be calculated by averaging…
We investigate a reversible polymerization process in which individual polymers aggregate and fragment at a rate proportional to their molecular weight. We find a nonequilibrium phase transition despite the fact that the dynamics are…
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…
We present a numerical study of the statistical properties of the potential energy landscape of a simple model for strong network-forming liquids. The model is a system of spherical particles interacting through a square well potential,…
Recently, nanofluidics experiments have been used to characterize the behavior of single DNA molecules confined to narrow slits etched with arrays of nanopits. Analysis of the experimental data relies on analytical estimates of the…
Landau's theory of phase transitions is adapted to treat independently relaxing regions in complex systems using nanothermodynamics. The order parameter we use governs the thermal fluctuations, not a specific static structure. We find that…
The review deals with a novel approach (MNEQT) to nonequilibrium thermodynamics (NEQT) that is based on the concept of internal equilibrium (IEQ) in an enlarged state space involving internal variables as additional state variables. The…
Various methods achieving importance sampling in ensembles of nonequilibrium trajectories enable to estimate free energy differences and, by maximum-likelihood post-processing, to reconstruct free energy landscapes. Here, based on Bayes…
Energy landscape theory describes how a full-length protein can attain its native fold after sampling only a tiny fraction of all possible structures. Although protein folding is now understood to be concomitant with synthesis on the…
The energy landscapes of proteins have evolved to be different from most random heteropolymers. Many studies have concluded that evolutionary selection for rapid and reliable folding to a given structure that is stable at biological…
We extend the non-parametric framework of reaction coordinate optimization to non-equilibrium ensembles of (short) trajectories. For example, we show how, starting from such an ensemble, one can obtain an equilibrium free energy profile…
In this work, a novel ring polymer representation for multi-level quantum system is proposed for thermal average calculations. The proposed presentation keeps the discreteness of the electronic states: besides position and momentum, each…